Molecular development of the mid-stage elongating cotton fiber

Cotton fiber is one of the leading natural textile fibers and is the leading value added crop in the USA. The annual business revenue from the cotton industry exceeds $120 billion. The growth of the cotton fiber is divided into four unique, yet overlapping stages; initiation, elongation, secondary wall biosynthesis and maturation. The quality of the cotton fiber quality is measured in terms of length and strength, which are primarily determined during elongation and secondary wall biosynthesis stages of growth. Here, we analyzed cotton fiber from Upland cotton cv. TM-1 (Gossypium hirsutum) at 11 and 17 days post-anthesis (DPA). Paired-end sequencing (Illumina MiSeq) generated 15 million reads from these two libraries and a unique cotton transcriptome database was created using the sequencing data from six stages fiber development (3, 5, 11, 17, 21, and 24 DPA), cotton community transcriptome and cotton D-genome. RNA-Seq analysis of 11 and 17 DPA tissues revealed 3391 differentially expressed transcripts. Annotation and putative gene functions were assigned to the contigs and known functions were mapped onto pathways using MapMan. Analysis showed differential expression of known marker genes for elongation (primarily down-regulated) and maturation (primarily up-regulated) along with a number of unknown genes. The molecular mechanisms of the pathways involved in elongation and maturation are investigated.